every time I try to download a mod since the past two days I've got this warning "This archive contains pugins in subdirectories, and will need a script attached for fomm to install it correctly." and it does this with every mod I tried to download in the last two days, what's causing this?

It means what it says, it has plugins in different subdirectories Usually mods packaged like this have optional plugins, that you need to choose what to use, without a FOMOD script FOMM doesn't know what plugins to use. This means that you can't install these mod with FOMM as they are, you either have to install them manually, or re-package the mod so that it has the same structure as Fallout 3's data folder.

how would I repackage it?